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Advances in Swine Transcriptomics

The past five years have seen a tremendous rise in porcine transcriptomic data. Available porcine Expressed Sequence Tags (ESTs) have expanded greatly, with over 623,000 ESTs deposited in Genbank. ESTs have been used to expand the pig-human comparative maps, but such data has also been used in many...

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Detalles Bibliográficos
Autores principales: Tuggle, Christopher K., Wang, Yanfang, Couture, Oliver
Formato: Texto
Lenguaje:English
Publicado: Ivyspring International Publisher 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802012/
https://www.ncbi.nlm.nih.gov/pubmed/17384733
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author Tuggle, Christopher K.
Wang, Yanfang
Couture, Oliver
author_facet Tuggle, Christopher K.
Wang, Yanfang
Couture, Oliver
author_sort Tuggle, Christopher K.
collection PubMed
description The past five years have seen a tremendous rise in porcine transcriptomic data. Available porcine Expressed Sequence Tags (ESTs) have expanded greatly, with over 623,000 ESTs deposited in Genbank. ESTs have been used to expand the pig-human comparative maps, but such data has also been used in many ways to understand pig gene expression. Several methods have been used to identify genes differentially expressed (DE) in specific tissues or cell types under different treatments. These include open screening methods such as suppression subtractive hybridization, differential display, serial analysis of gene expression, and EST sequence frequency, as well as closed methods that measure expression of a defined set of sequences such as hybridization to membrane arrays and microarrays. The use of microarrays to begin large-scale transcriptome analysis has been recently reported, using either specialized or broad-coverage arrays. This review covers published results using the above techniques in the pig, as well as unpublished data provided by the research community, and reports on unpublished Affymetrix data from our group. Published and unpublished bioinformatics efforts are discussed, including recent work by our group to integrate two broad-coverage microarray platforms. We conclude by predicting experiments that will become possible with new anticipated tools and data, including the porcine genome sequence. We emphasize that the need for bioinformatics infrastructure to efficiently store and analyze the expanding amounts of gene expression data is critical, and that this deficit has emerged as a limiting factor for acceleration of genomic understanding in the pig.
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spelling pubmed-18020122007-03-23 Advances in Swine Transcriptomics Tuggle, Christopher K. Wang, Yanfang Couture, Oliver Int J Biol Sci Review The past five years have seen a tremendous rise in porcine transcriptomic data. Available porcine Expressed Sequence Tags (ESTs) have expanded greatly, with over 623,000 ESTs deposited in Genbank. ESTs have been used to expand the pig-human comparative maps, but such data has also been used in many ways to understand pig gene expression. Several methods have been used to identify genes differentially expressed (DE) in specific tissues or cell types under different treatments. These include open screening methods such as suppression subtractive hybridization, differential display, serial analysis of gene expression, and EST sequence frequency, as well as closed methods that measure expression of a defined set of sequences such as hybridization to membrane arrays and microarrays. The use of microarrays to begin large-scale transcriptome analysis has been recently reported, using either specialized or broad-coverage arrays. This review covers published results using the above techniques in the pig, as well as unpublished data provided by the research community, and reports on unpublished Affymetrix data from our group. Published and unpublished bioinformatics efforts are discussed, including recent work by our group to integrate two broad-coverage microarray platforms. We conclude by predicting experiments that will become possible with new anticipated tools and data, including the porcine genome sequence. We emphasize that the need for bioinformatics infrastructure to efficiently store and analyze the expanding amounts of gene expression data is critical, and that this deficit has emerged as a limiting factor for acceleration of genomic understanding in the pig. Ivyspring International Publisher 2007-02-09 /pmc/articles/PMC1802012/ /pubmed/17384733 Text en © Ivyspring International Publisher. This is an open-access article distributed under the terms of the Creative Commons License (http://creativecommons.org/licenses/by-nc-nd/3.0/). Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited.
spellingShingle Review
Tuggle, Christopher K.
Wang, Yanfang
Couture, Oliver
Advances in Swine Transcriptomics
title Advances in Swine Transcriptomics
title_full Advances in Swine Transcriptomics
title_fullStr Advances in Swine Transcriptomics
title_full_unstemmed Advances in Swine Transcriptomics
title_short Advances in Swine Transcriptomics
title_sort advances in swine transcriptomics
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802012/
https://www.ncbi.nlm.nih.gov/pubmed/17384733
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